So, the engine manufacturers are completely in the clear, eh?
I suppose that depends on what the standard assembly process is and why/if Boeing mechanics pulled the original filters.
If this is, as some have suggested, a standard procedure (replace filters after a few hours of engine run), then there should be some job paperwork and QA signoff covering it.[1]
If this was done for some out of sequence reason, then there is (was, back in my day) a series of LRU replacement procedures one must follow to do the work and ensure things got put back together again.[2]
[1] Back in the '90s, Boeing made an attempt to adopt the Japanese (Toyota) just-in-time manufacturing processes. One feature of this is that, for planned work, tools and parts are provided in job-specific containers (or tracking). So the mechanic would be issues new filters along with the job paperwork. Nobody runs off to the supply window to fetch the filters mid job. So leaving the job with a couple of 'spare parts' should have more than a few eyebrows raised.
[2] One of my jobs at Boeing was to put in place an LRU test system, which provides the shop floor with a set of instructions needed to do troubleshooting and get things put back together correctly again. When I left, the process we had in place was very fast and efficient. But the IT people love to re-engineer stuff, so our system was one of many due to be overhauled. Whether they got it right or not, I can't say. Also, out of sequence work is anathema to the schedule driven world of management. There are two ways of handling it: Make it fast and simple so as to get it over with in a minimum of time. Or make the shop floor people jump through numerous management hoops to discourage 'extra' work. Here again, our approach was to keep it simple. But I can't say if things changed in the decade where I wasn't able to keep an eye on the place.